Source code for gromacs.pdb2gmx

#!/usr/bin/env python3

"""Module containing the Pdb2gmx class and the command line interface."""
import os
import argparse
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_md.gromacs.common import get_gromacs_version
from biobb_md.gromacs.common import GromacsVersionError


[docs]class Pdb2gmx(BiobbObject): """ | biobb_md Pdb2gmx | Wrapper class for the `GROMACS pdb2gmx <http://manual.gromacs.org/current/onlinehelp/gmx-pdb2gmx.html>`_ module. | The GROMACS pdb2gmx module, reads a .pdb (or .gro) file, reads some database files, adds hydrogens to the molecules and generates coordinates in GROMACS (GROMOS), or optionally .pdb, format and a topology in GROMACS format. These files can subsequently be processed to generate a run input file. Args: input_pdb_path (str): Path to the input PDB file. File type: input. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/data/gromacs/egfr.pdb>`_. Accepted formats: pdb (edam:format_1476). output_gro_path (str): Path to the output GRO file. File type: output. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/reference/gromacs/ref_pdb2gmx.gro>`_. Accepted formats: gro (edam:format_2033). output_top_zip_path (str): Path the output TOP topology in zip format. File type: output. `Sample file <https://github.com/bioexcel/biobb_md/raw/master/biobb_md/test/reference/gromacs/ref_pdb2gmx.zip>`_. Accepted formats: zip (edam:format_3987). properties (dict - Python dictionary object containing the tool parameters, not input/output files): * **water_type** (*str*) - ("spce") Water molecule type. Values: spc, spce, tip3p, tip4p, tip5p, tips3p. * **force_field** (*str*) - ("amber99sb-ildn") Force field to be used during the conversion. Values: gromos45a3, charmm27, gromos53a6, amber96, amber99, gromos43a2, gromos54a7, gromos43a1, amberGS, gromos53a5, amber99sb, amber03, amber99sb-ildn, oplsaa, amber94. * **ignh** (*bool*) - (False) Should pdb2gmx ignore the hidrogens in the original structure. * **his** (*str*) - (None) Histidine protonation array. * **merge** (*bool*) - (False) Merge all chains into a single molecule. * **gmx_lib** (*str*) - (None) Path set GROMACS GMXLIB environment variable. * **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. * **container_path** (*str*) - (None) Path to the binary executable of your container. * **container_image** (*str*) - ("gromacs/gromacs:latest") Container Image identifier. * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container. * **container_working_dir** (*str*) - (None) Path to the internal CWD in the container. * **container_user_id** (*str*) - (None) User number id to be mapped inside the container. * **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell. Examples: This is a use example of how to use the building block from Python:: from biobb_md.gromacs.pdb2gmx import pdb2gmx prop = { 'his': '0 0 1 1 0 0 0' } pdb2gmx(input_pdb_path='/path/to/myStructure.pdb', output_gro_path='/path/to/newStructure.gro', output_top_zip_path='/path/to/newTopology.zip', properties=prop) Info: * wrapped_software: * name: GROMACS Pdb2gmx * version: >5.1 * license: LGPL 2.1 * ontology: * name: EDAM * schema: http://edamontology.org/EDAM.owl """ def __init__(self, input_pdb_path: str, output_gro_path: str, output_top_zip_path: str, properties: dict = None, **kwargs) -> None: properties = properties or {} # Call parent class constructor super().__init__(properties) # Input/Output files self.io_dict = { "in": {"input_pdb_path": input_pdb_path}, "out": {"output_gro_path": output_gro_path, "output_top_zip_path": output_top_zip_path} } # Properties specific for BB self.internal_top_name = properties.get('internal_top_name', 'p2g.top') # Excluded from documentation for simplicity self.internal_itp_name = properties.get('internal_itp_name', 'posre.itp') # Excluded from documentation for simplicity self.water_type = properties.get('water_type', 'spce') self.force_field = properties.get('force_field', 'amber99sb-ildn') self.ignh = properties.get('ignh', False) self.his = properties.get('his', None) self.merge = properties.get('merge', False) # Properties common in all GROMACS BB self.gmx_lib = properties.get('gmx_lib', None) self.gmx_path = properties.get('gmx_path', 'gmx') self.gmx_nobackup = properties.get('gmx_nobackup', True) self.gmx_nocopyright = properties.get('gmx_nocopyright', True) if self.gmx_nobackup: self.gmx_path += ' -nobackup' if self.gmx_nocopyright: self.gmx_path += ' -nocopyright' if not self.container_path: self.gmx_version = get_gromacs_version(self.gmx_path) # Check the properties self.check_properties(properties)
[docs] @launchlogger def launch(self) -> int: """Execute the :class:`Pdb2gmx <gromacs.pdb2gmx.Pdb2gmx>` object.""" # Setup Biobb if self.check_restart(): return 0 self.stage_files() internal_top_name = fu.create_name(prefix=self.prefix, step=self.step, name=self.internal_top_name) internal_itp_name = fu.create_name(prefix=self.prefix, step=self.step, name=self.internal_itp_name) # Create command line self.cmd = [self.gmx_path, "pdb2gmx", "-f", self.stage_io_dict["in"]["input_pdb_path"], "-o", self.stage_io_dict["out"]["output_gro_path"], "-p", internal_top_name, "-water", self.water_type, "-ff", self.force_field, "-i", internal_itp_name] if self.his: self.cmd.append("-his") self.cmd = ['echo', self.his, '|'] + self.cmd if self.ignh: self.cmd.append("-ignh") if self.merge: self.cmd.append("-merge") self.cmd.append("all") if self.gmx_lib: self.environment = os.environ.copy() self.environment['GMXLIB'] = self.gmx_lib # Check GROMACS version if not self.container_path: if self.gmx_version < 512: raise GromacsVersionError("Gromacs version should be 5.1.2 or newer %d detected" % self.gmx_version) fu.log("GROMACS %s %d version detected" % (self.__class__.__name__, self.gmx_version), self.out_log) # Run Biobb block self.run_biobb() # Copy files to host self.copy_to_host() if self.container_path: internal_top_name = os.path.join(self.stage_io_dict.get("unique_dir"), internal_top_name) # zip topology fu.log('Compressing topology to: %s' % self.io_dict["out"]["output_top_zip_path"], self.out_log, self.global_log) fu.zip_top(zip_file=self.io_dict["out"]["output_top_zip_path"], top_file=internal_top_name, out_log=self.out_log) # Remove temporal files self.tmp_files.extend([self.internal_top_name, self.internal_itp_name, self.stage_io_dict.get("unique_dir")]) self.remove_tmp_files() return self.return_code
[docs]def pdb2gmx(input_pdb_path: str, output_gro_path: str, output_top_zip_path: str, properties: dict = None, **kwargs) -> int: """Create :class:`Pdb2gmx <gromacs.pdb2gmx.Pdb2gmx>` class and execute the :meth:`launch() <gromacs.pdb2gmx.Pdb2gmx.launch>` method.""" return Pdb2gmx(input_pdb_path=input_pdb_path, output_gro_path=output_gro_path, output_top_zip_path=output_top_zip_path, properties=properties, **kwargs).launch()
[docs]def main(): """Command line execution of this building block. Please check the command line documentation.""" parser = argparse.ArgumentParser(description="Wrapper of the GROMACS pdb2gmx module.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string") # Specific args of each building block required_args = parser.add_argument_group('required arguments') required_args.add_argument('--input_pdb_path', required=True) required_args.add_argument('--output_gro_path', required=True) required_args.add_argument('--output_top_zip_path', required=True) args = parser.parse_args() config = args.config if args.config else None properties = settings.ConfReader(config=config).get_prop_dic() # Specific call of each building block pdb2gmx(input_pdb_path=args.input_pdb_path, output_gro_path=args.output_gro_path, output_top_zip_path=args.output_top_zip_path, properties=properties)
if __name__ == '__main__': main()